ENH update figure4

Author: cocodyq

General_Scripts/10_Transmembrane_secreted/02_Compare between archaea and bacteria/05_count_cog_class_trans.py

@@ -56,9 +56,9 @@ def count_class(trans,seq_cogs,outfile):
 
 infile = '90AA_tm_signal.tsv'
 infile1 = '0_arc_motif_cog.tsv'
-outfile1 = '1_arc_motif_cog_class_count_trans.tsv'
+outfile1 = '2_arc_motif_cog_class_count_trans.tsv'
 infile2 = '0_bac_motif_cog.tsv'
-outfile2 = '1_bac_motif_cog_class_count_trans.tsv'
+outfile2 = '2_bac_motif_cog_class_count_trans.tsv'
 
 trans = store(infile)
 seq_cogs = merge_class(infile1)

General_Scripts/10_Transmembrane_secreted/02_Compare between archaea and bacteria/06_count_cog_trans.py

@@ -62,10 +62,10 @@ def count_bac(infile1,infile2,outfile1,outfile2):
 outfile3 = '0_bac_motif_cog_trans.tsv'
 outfile4 = '0_bac_motif_cog_not_trans.tsv'
 
-outfile5 = '1_arc_motif_cog_count_trans.tsv'
-outfile6 = '1_arc_motif_cog_count_not_trans.tsv'
-outfile7 = '1_bac_motif_cog_count_trans.tsv'
-outfile8 = '1_bac_motif_cog_count_not_trans.tsv'
+outfile5 = '9_arc_motif_cog_count_trans.tsv'
+outfile6 = '9_arc_motif_cog_count_not_trans.tsv'
+outfile7 = '9_bac_motif_cog_count_trans.tsv'
+outfile8 = '9_bac_motif_cog_count_not_trans.tsv'
 
 trans = store(infile)
 split(trans,infile1,outfile1,outfile2)

General_Scripts/10_Transmembrane_secreted/Readme.md

@@ -16,5 +16,5 @@
 | 02_extract_cog.py | Extract bacterial and archaeal 90AA families with COG annotation | 90AA_tax.tsv.xz 1_cdd_tcov_90AA.tsv.gz cddid_all.tbl cog-20.def.tab.tsv | 0_arc_motif_cog.tsv 0_bac_motif_cog.tsv 0_bg_motif_cog.tsv |
 | 03_count_cog_class.py | Count the number of each COG class of smORFs | 0_bac_motif_cog.tsv 0_arc_motif_cog.tsv 0_bg_motif_cog.tsv | 1_bac_motif_cog_class_count.tsv 1_arc_motif_cog_class_count.tsv 1_bg_motif_cog_class_count.tsv |
 | 04_count_cog.py | Count the number of each COG of smORFs | 0_arc_motif_cog.tsv 0_bg_motif_cog.tsv | 1_arc_motif_cog_count.tsv 1_bg_motif_cog_count.tsv_new |
-| 05_count_cog_class_trans.py | Count number of each cog class number of transmembrane or secreted smORFs | 90AA_tm_signal.tsv 0_arc_motif_cog.tsv 0_bac_motif_cog.tsv | 1_arc_motif_cog_class_count_trans.tsv 1_bac_motif_cog_class_count_trans.tsv |
-| 06_count_cog_trans.py | Count number of each COG of transmembrane or secreted smORFs | 90AA_tm_signal.tsv.gz 90AA_tm_signal.tsv.gz 0_arc_motif_cog.tsv 0_bac_motif_cog.tsv | 1_arc_motif_cog_count_trans.tsv 1_arc_motif_cog_count_not_trans.tsv 1_bac_motif_cog_count_trans.tsv 1_bac_motif_cog_count_not_trans.tsv |
+| 05_count_cog_class_trans.py | Count number of each cog class number of transmembrane or secreted smORFs | 90AA_tm_signal.tsv 0_arc_motif_cog.tsv 0_bac_motif_cog.tsv | 2_arc_motif_cog_class_count_trans.tsv 2_bac_motif_cog_class_count_trans.tsv |
+| 06_count_cog_trans.py | Count number of each COG of transmembrane or secreted smORFs | 90AA_tm_signal.tsv.gz 0_arc_motif_cog.tsv 0_bac_motif_cog.tsv | 9_arc_motif_cog_count_trans.tsv 9_arc_motif_cog_count_not_trans.tsv 9_bac_motif_cog_count_trans.tsv 9_bac_motif_cog_count_not_trans.tsv |